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Computational Chemistry

Video: Getting up close and personal with molecules in virtual reality

New VR tools promise better understanding and collaboration for chemists

by Sam Lemonick
July 12, 2021

Credit: Darren Weaver/ACS Productions/C&EN

Virtual-reality tools let chemists explore proteins and molecules, build and test potential drugs, and collaborate with colleagues remotely. In this video, C&EN reporter Sam Lemonick tries out a VR app that incorporates visualizations of molecules with advanced computational tools—offering a new way for chemists to develop drugs and address other problems—and learns how VR could help scientists use robotic lab equipment. Researchers who are using VR to study SARS-CoV-2 say the tools are giving them new insights about the virus and vaccines. But one scientist cautions the cost of VR equipment could limit its potential to address global problems.

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The following is an edited transcript of the video. We have edited the interviews within for length and clarity.

Sam Lemonick (voice over): Virtual reality is giving chemists a new way to see and interact with atoms and molecules.

Steve McCloskey: You can just reach out and grab with that middle finger.

Sam (in interview): Wow, that’s really cool. I can just grab on to any part of this and spin it around in space. And I can walk around it too like it’s just, as if it’s just sitting on the table in front of me.

Steve: Yeah definitely.

Sam (voice over): Yup, that’s me. Sam Lemonick.

That clip was filmed in an app called Nanome. And that’s CEO and one of the founders Steve McCloskey giving me a tour of their platform.

In virtual reality, chemists can pick up a molecule, climb inside a protein binding pocket, and see chemistry in a way they never have before.

Many of the VR chemistry apps on the market are focused on teaching chemistry to students. Other groups—including the Nanome team—are thinking about ways to incorporate VR into chemistry and drug research.

VR has already proved useful to some researchers who are studying the coronavirus that causes COVID-19.

Michael (Mike) Kuiper: When I was first told about VR I thought, “Oh why would we bother, what is the kind of add to this.” A funny story about this was someone goaded me to try it, so we have VR machines here, so I installed the software and got it running on a Friday night, late at night. By Saturday morning I’d gone to the hardware store and bought my own set, it was that compelling and I realized it was the game changer for me.

Sam: Mike and his colleague Vasan are using Nanome to study the coronavirus’s spike protein, which is the part of the virus that first attacks our cells. It is also the part vaccines use to trigger our immune system. They can model the protein on high-performance computers and then visualize it in VR, zooming in on structural aspects to try to predict how it will behave in the body.

Mike: By manipulating these objects in your hand it gives you a very intuitive feel for how these proteins behave. You start to notice things in VR that I don’t think you notice on a 2D screen.

Sam: Mike noted that VR could highlight structural differences among virus variants that might change the effectiveness of a vaccine.

So why are these researchers so excited about VR? Let’s take a look.

Sam: In Nanome’s app, chemists can construct molecules from scratch.

Steve: You can start with something like this cyclohexane and then just build out, adding any kind of structures that you want.

Sam: Chemists can also examine molecules from big public collections like the Protein Data Bank.

Steve: All you need to know is the code. So 1tyl. They have this four-digit code system, and then boom, you just load it.

Sam: The novelty of standing inside a protein binding pocket was cool even to me, a nonscientist. But Nanome also lets users mesh VR visualization with high-level calculations that can help them understand how a drug molecule might work inside our bodies and figure out ways to optimize it.

As exciting as these tools may be, Vasan noted that the cost of a VR system is currently a barrier to widespread use. He predicts the technology will have its biggest impact on chemistry research when it’s more widely accessible. When we talked in May, he said it would be helpful if researchers had VR tools in India, where a new coronavirus variant had been rapidly spreading.

Vasan Vasan: If everyone is having the same level of access, collaboration becomes a lot easier.

Sam: Beyond understanding how molecules behave, VR can also serve a more practical purpose, such as helping chemists who are used to hands-on lab work get more comfortable with unfamiliar systems.

For example, computational chemist Lee Cronin and his team are developing a system they call the “Chemputer,” which involves a combination of lab equipment and software.

Lee thinks chemists could use VR to test-drive the Chemputer or plan reactions, verifying the process and results before loading in expensive reagents. Or they could use VR to operate the instruments remotely.

Lee hopes tools like these will enable chemists to spend less time at the lab bench and more time thinking about reactions. Whether folks are building a robot to do experiments or trying to fight a global pandemic, these app developers are excited to see how VR may augment scientific discovery.



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